Multiple sequence alignment - TraesCS5D01G507200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G507200 chr5D 100.000 2608 0 0 1 2608 532625856 532628463 0.000000e+00 4817.0
1 TraesCS5D01G507200 chr7D 98.393 2613 31 6 1 2608 530382800 530380194 0.000000e+00 4582.0
2 TraesCS5D01G507200 chr7D 98.391 2611 32 8 1 2608 460098817 460101420 0.000000e+00 4580.0
3 TraesCS5D01G507200 chr3D 98.391 2610 36 5 1 2605 360365408 360368016 0.000000e+00 4582.0
4 TraesCS5D01G507200 chr3D 98.354 2612 30 6 1 2608 166983439 166986041 0.000000e+00 4573.0
5 TraesCS5D01G507200 chr3D 98.200 2611 41 5 1 2608 2046103 2043496 0.000000e+00 4556.0
6 TraesCS5D01G507200 chr4D 98.319 2618 33 7 1 2608 338461877 338464493 0.000000e+00 4580.0
7 TraesCS5D01G507200 chr1D 97.709 2619 45 9 3 2608 419200471 419203087 0.000000e+00 4490.0
8 TraesCS5D01G507200 chr1D 98.000 50 1 0 1 50 303046114 303046065 1.290000e-13 87.9
9 TraesCS5D01G507200 chr6D 97.480 2619 46 9 3 2608 6286937 6284326 0.000000e+00 4453.0
10 TraesCS5D01G507200 chr2D 97.708 2574 49 8 42 2608 612830237 612827667 0.000000e+00 4418.0
11 TraesCS5D01G507200 chr7B 90.141 142 4 1 3 134 986200 986341 2.670000e-40 176.0
12 TraesCS5D01G507200 chr5A 96.923 65 2 0 1 65 647457461 647457525 2.740000e-20 110.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G507200 chr5D 532625856 532628463 2607 False 4817 4817 100.000 1 2608 1 chr5D.!!$F1 2607
1 TraesCS5D01G507200 chr7D 530380194 530382800 2606 True 4582 4582 98.393 1 2608 1 chr7D.!!$R1 2607
2 TraesCS5D01G507200 chr7D 460098817 460101420 2603 False 4580 4580 98.391 1 2608 1 chr7D.!!$F1 2607
3 TraesCS5D01G507200 chr3D 360365408 360368016 2608 False 4582 4582 98.391 1 2605 1 chr3D.!!$F2 2604
4 TraesCS5D01G507200 chr3D 166983439 166986041 2602 False 4573 4573 98.354 1 2608 1 chr3D.!!$F1 2607
5 TraesCS5D01G507200 chr3D 2043496 2046103 2607 True 4556 4556 98.200 1 2608 1 chr3D.!!$R1 2607
6 TraesCS5D01G507200 chr4D 338461877 338464493 2616 False 4580 4580 98.319 1 2608 1 chr4D.!!$F1 2607
7 TraesCS5D01G507200 chr1D 419200471 419203087 2616 False 4490 4490 97.709 3 2608 1 chr1D.!!$F1 2605
8 TraesCS5D01G507200 chr6D 6284326 6286937 2611 True 4453 4453 97.480 3 2608 1 chr6D.!!$R1 2605
9 TraesCS5D01G507200 chr2D 612827667 612830237 2570 True 4418 4418 97.708 42 2608 1 chr2D.!!$R1 2566

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
34 35 2.414161 CGTGTCAGAGATCGTACTTGCA 60.414 50.000 0.00 0.0 0.00 4.08 F
541 575 2.545731 TGCATCGAAGCGCATTACTTA 58.454 42.857 11.47 0.0 37.31 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1310 0.678048 GCTTCCGGTCCTTCTGCAAT 60.678 55.0 0.0 0.0 0.0 3.56 R
1813 1848 0.915872 TGGGGACTCTGCCATCACAT 60.916 55.0 0.0 0.0 0.0 3.21 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.414161 CGTGTCAGAGATCGTACTTGCA 60.414 50.000 0.00 0.00 0.00 4.08
103 114 3.523606 TGCATGCATAATGGTTTCCAC 57.476 42.857 18.46 0.00 35.80 4.02
142 166 6.157211 TGAATGTTTTTACGGTTTTGTGTGT 58.843 32.000 0.00 0.00 0.00 3.72
143 167 6.089551 TGAATGTTTTTACGGTTTTGTGTGTG 59.910 34.615 0.00 0.00 0.00 3.82
144 168 4.868067 TGTTTTTACGGTTTTGTGTGTGT 58.132 34.783 0.00 0.00 0.00 3.72
145 169 4.680110 TGTTTTTACGGTTTTGTGTGTGTG 59.320 37.500 0.00 0.00 0.00 3.82
146 170 4.500603 TTTTACGGTTTTGTGTGTGTGT 57.499 36.364 0.00 0.00 0.00 3.72
147 171 3.473093 TTACGGTTTTGTGTGTGTGTG 57.527 42.857 0.00 0.00 0.00 3.82
291 320 3.066760 GCATGTATCAAACCAAGTAGCCC 59.933 47.826 0.00 0.00 0.00 5.19
463 494 4.202441 GCTTCTGTGATATGTGGTTGGAT 58.798 43.478 0.00 0.00 0.00 3.41
541 575 2.545731 TGCATCGAAGCGCATTACTTA 58.454 42.857 11.47 0.00 37.31 2.24
796 830 7.547370 ACAAGTCATTTCCGAAGAGATTAGAAG 59.453 37.037 0.00 0.00 0.00 2.85
1275 1310 4.321899 GGCTACAAGGAAATGCATCAAACA 60.322 41.667 0.00 0.00 0.00 2.83
1798 1833 2.232941 ACCCACTGTCGACGTTTCATAT 59.767 45.455 11.62 0.00 0.00 1.78
1813 1848 6.597672 ACGTTTCATATGCAGGATAAGAAACA 59.402 34.615 27.94 5.72 46.39 2.83
1949 1984 0.250727 AGCAGGTAACAACACCGCAT 60.251 50.000 10.24 0.00 43.84 4.73
2126 2162 5.451798 GCAGAAGTCAGAATTTTTGAACCCA 60.452 40.000 0.00 0.00 0.00 4.51
2351 2387 2.173143 AGAACTACGGGTTGTTTTCCCA 59.827 45.455 0.92 0.00 44.81 4.37
2377 2413 3.686726 GTGACATTGATCCAGAGGTTCAC 59.313 47.826 0.00 0.00 32.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.917088 CCATGAAGAAAGTTTGGGATTATACAT 58.083 33.333 0.00 0.00 0.00 2.29
103 114 3.137533 ACATTCAAAATTTTGCCCCACG 58.862 40.909 23.36 11.79 38.05 4.94
158 186 1.134189 GGCATGTACCCTGAACCCTAC 60.134 57.143 0.00 0.00 0.00 3.18
463 494 4.002506 ATGTGCACTGACCGCGGA 62.003 61.111 35.90 9.83 0.00 5.54
771 805 7.761704 TCTTCTAATCTCTTCGGAAATGACTTG 59.238 37.037 0.00 0.00 0.00 3.16
796 830 4.199310 TCAACTATGGCAAAGGCTGTATC 58.801 43.478 0.00 0.00 40.87 2.24
1275 1310 0.678048 GCTTCCGGTCCTTCTGCAAT 60.678 55.000 0.00 0.00 0.00 3.56
1798 1833 4.641541 CCATCACATGTTTCTTATCCTGCA 59.358 41.667 0.00 0.00 0.00 4.41
1813 1848 0.915872 TGGGGACTCTGCCATCACAT 60.916 55.000 0.00 0.00 0.00 3.21
1973 2008 4.219115 TCAATGAGTAAAGGGGCAAACAA 58.781 39.130 0.00 0.00 0.00 2.83
2065 2101 1.126488 ATGCTCTCGGGACATGTGAT 58.874 50.000 1.15 0.00 0.00 3.06
2126 2162 3.162666 TGAGATCGTAGGTCACTTTGGT 58.837 45.455 0.00 0.00 0.00 3.67
2351 2387 2.240667 CCTCTGGATCAATGTCACCCTT 59.759 50.000 0.00 0.00 0.00 3.95


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.